Rubbish Resources: Turning waste into useful products.

Firstly, a huge thank you to The Royal Society of Biology for sponsoring this event, which is part of ThRSB-logoe Royal Society of Chemistry-funded Green Reactions project.

Friday 19th June brought us the third in our ongoing series of public dialogues, this time exploring the concepts of using engineered organisms to remove pollutants from the environment and the transformation of waste biomass into useful products as part of a future bio-based economy.

Ruth Haley spoke first about her work, as part of the iGEM project, genetically engineering E. coli to take up toxic cadmium pollution from coastlines contaminated by mining work in the 1950s. As well as introducing the uses of synthetic biology and genetic modification within food production, as biomarkers (a protein that is used to show the expression of a specific gene) and in solving some worldwide issues.

Ruth talks about using engineered bacteria to sort out heavy metals pollution to a packed Basement audience.
Ruth talks about using engineered bacteria to sort out heavy metals pollution to a packed Basement audience.

Ruth was followed by Emily Johnston from the biology department’s Centre for Novel Agricultural Products (CNAP). Continuing the theme of pollution remediation, Emily described how contamination by toxic explosives residues, and in particular TNT and RDX, is a serious issue in places like military training ranges. She went on to talk about how she was able to solve the mystery of why a mutant plant from the CNAP laboratory was able to survive in soil contaminated with TNT where most plants died and how this knowledge could now be used to decontaminate explosives-polluted land by dropping “seed balls” of genetically engineered plants from helicopters.

The Rubbish Resources speakers and Chair (L to R: Ruth Haley, Emily Johnston, Iris Houthoff, Ian Ingram and Nicky Egan.
The Rubbish Resources speakers and Chair (L to R: Ruth Haley, Emily Johnston, Iris Houthoff, Ian Ingram and Nicky Egan.

After a short break for more beer, Ian Ingram and Nicky Egan from the Green Chemistry Centre outlined the concepts behind the bio-based economy of the future using waste carbon dioxide and waste plant material (biomass) as sources of carbon in place of fossil resources. Ian spoke about the opportunities to create new plastics from bio-derived “platform molecules”, some pleasant-smelling examples of which he bought along to sniff! Nicky talked about how one of the most abundant and reluctant bio-molecules, lignin, which gives woody plants their rigidity, can be processed using microwaves to give useful bio-based antioxidants, which can be used to prolong the life of motor oils and other products.

The panel take questions from the audience.
The panel take questions from the audience.

After the talks we held a questions and discussion session with all the speakers forming a panel to discuss the issues. A selection of questions (slightly edited to combine similar questions), and our speakers’ answers to them, are given below:

Question for Emily and Ruth:

Would you say the problem with GM is one of public relations rather than science? Even more conventional hybrid crops took a while to be accepted – isn’t there a need to communicate better and reduce sensationalism?


Agreed, there needs to be better communication between scientists and the general public as to what they are doing, the precautions they have put in place and the testing that the products have been through. We need more education about transgenic organisms and synthetic biology so that people are not frightened of the unknown. This has to include the politicians too!

It’s important to get people talking about science and improve the quality of science journalism. Too often science news stories miss the point or go after a sensationalist headline at the expense of actually informing their readers. Scientists talking to the public at this kind of event are a key part of this.


I agree completely, it’s part of human nature to question the new and that’s a good thing.  We are always right to question new technologies and look at things critically.  Mis-reporting by press is a big issue, as readers won’t have time to investigate things further, never mind paying for a subscription to the scientific journal where the research was originally published with specialised jargon.  Something that terrifies scientists is when results are misinterpreted and/or sensationalised into something they’re not.  Combating misinterpretation of science in the press is something that we can all help with though; Sense About Science is a charity which challenges poor science reporting, and we can help just by emailing them if we see something suspicious in the press or in advertising.  On the topic of GM, in 2009 they published a document “Making Sense of GM” which is really helpful.  Copies of this can be ordered for free through the link below.

Re. GM, last year, at the request of Government, the Council for Science and Technology wrote a report on the risks and benefits of GM technologies, and what might be done to raise the quality of debate, decision-making and regulation at UK and European levels.  This is also very informative and is available through this link.

Chemicals that are insoluble are more dangerous for the environment than soluble ones?


This is a really interesting question. Water solubility of a pollutant in the environment can be an issue as it increases the risk of the pollutant draining down into underwater aquifers, and getting into water supplies. On the other hand, chemicals which are not very water soluble can become bioaccumulated, as they’re more easily stored in cells.  This means that it’s easier for water insoluble chemicals to increase in amount within an organism, to a level where they’re more likely to cause harm.  In terms of explosives pollution, clean-up of Royal Demolition Explosive is a greater priority over TNT, as there has already been a case of this water-soluble chemical getting into an underwater aquifer in Massachusetts.


In the case of cadmium – the cadmium being soluble in the sea is an issue for the marine life, but it being in the soil at all (in both soluble and insoluble forms) is an issue for the species on the land.

This contamination is an issue in both forms. Sometimes only a soluble form of a pollutant would be an issue dependent on what happens when the insoluble form reacts with water (the species may be charged or change the pH etc).

Questions for Ruth:

How could the cadmium granules from your bacteria capture be extracted? Could it be reused?

The iGEM team did not get as far as to develop a way of extracting the cadmium from the bacteria. The easiest way would be to remove the bacteria from the bioreactor and then to lyse (break open) the cells releasing the cadmium into a vessel in a lab then isolate the cadmium from the cell lysate. That’s work that is still ongoing at the moment but the cadmium, once pure, could be reused in products like batteries. Cadmium is pretty toxic though so these days we’re trying to use less of it in applications where it might be dissipated into the environment.

Did you try your method in the field?

No, this would take many more years. The first step would be to get the system working and experiment with the system to see what concentrations of cadmium the bacteria would tolerate. The proof-of-concept organism that we produced would probably go through a lot of iterations before being put in the field. We’d have to start by exposing the bacteria to samples of the seawater and solid matter from the bay in the lab environment and gradually introduce more factors such as salinity, temperature, water flowrate etc to make sure the system works properly under realistic conditions before testing in the field.

Is it safe to use this engineered bacterial system?

Honestly, at the moment we can’t be completely sure for our specific system, which is why there would have to be a lot of laboratory work done on the whole setup – to make sure the bacteria stay where they’re supposed to be and we don’t end up unintentionally releasing any of the cadmium we collect – before it could be tested in the field. It is worth remembering that E. Coli is a very common bacteria though, you’ve got millions of them on and in your body right now, and although we’d have to check carefully before field use there’s no reason to think that our modification has made it harmful.

Are the bacteria reproductive? Does the “GM” get transmitted to offspring?

The DNA is taken up in a plasmid into the bacteria. This means that when the bacteria replicate their genome prior to binary fission the plasmid is also replicated (in most cases). This means that the GM DNA is carried on through the generations. Engineering the bacteria so they didn’t reproduce would mean we couldn’t make enough to make the population sizes required for their application into the systems we are developing.

It is possible, if their getting into the environment is enough of a problem to justify it, to further engineer the bacteria with a “kill switch”. This could be done by making them dependent on some factor that is provided to them in the bio-reactor but which doesn’t occur outside in nature, so the cells would die if they were accidentally released.

Questions for Ian:

How long will it take to switch from petroleum to bio-based resources? Is there industrial/commercial support for the biorefinery and biobased products?

 In some regards the change is already happening and bio-based products are already on the market. Coke recently produced partially bio-based PET “Plantbottles” where the ethylene glycol monomer, derived from biomass, is combined with petrochemical terephthalic acid. Bayer, a pretty big and serious chemicals company, is using their “Dream” process to add some carbon dioxide into the polyols they use to make polyurethane foams, and Ford have been using soybean oil derived polyols in car seats for a while now. Obviously there’s a long way to go but change is coming, and with many big industrial concerns already moving towards bio-based products there is quite a bit of momentum already.

What is the (environmental and economic) cost of biofuels? Will they compete with fossil fuels? Do biofuels have to be made from food crops? Is there enough biomass available?

 The idea behind using biofuels is that plants take carbon dioxide from the atmosphere and turn it into biomass by photosynthesis, when this is converted into fuels and burnt, that carbon dioxide is released again so the process is potentially carbon-neutral, although the energy requirements for harvesting and processing the biomass need to be considered. As things stand the major biofuels in use are bioethanol and biodiesel and in many parts of the world these are already available at the petrol stations by themselves or as blends with conventional fuels.

Bioethanol is made by fermentation of sugars with yeast in the same way as alcoholic drinks and currently this is done on a large scale in places like Brazil from sugarcane. Conventional biodiesel is made by trans-esterification of plant or animal fats with methanol, at the moment palm and soybean oil are the most important feedstocks for this. Obviously both sugarcane and soybean oil are foodstuffs, sometimes called “first generation biomass”, and inevitably demand for these products pushes up food prices and competes for agricultural land with food production. However, there is a lot of work being done to use “second generation” biomass, which is cellulosic material from agricultural waste like wheat straw or the stalks of oil seed rape, for ethanol production. As these are the inedible by-products of growing food crops, using these might actually make food production more profitable! Similarly, there is a lot of work being done on using oils from bacteria or algae to make biodiesel instead of land based crops to reduce competition with food. In terms of scale, there are vast quantities of cellulosic waste available at almost no cost.

One of the hot topics in sustainable science is how to store any surplus renewable energy on sunny, windy days when wind, solar and other “green” sources of energy produce more than we are using. One interesting method that has been suggested is to use the excess electricity to make hydrogen from water by electrolysis and then use the hydrogen to make methanol by combining it with carbon dioxide. Since methanol is a liquid it is easier to store than hydrogen and could be burnt to generate electricity when renewables do not provide enough power. Methanol can also be used as the basis for a lot of other chemicals, including fuels for vehicles like dimethyl ether, and some people believe in the “methanol economy” being a big part of a sustainable future.


What is the biomass:CO2  ratio in the final plastics? How does recycling of biobased plastics work? What are they recycled into?

 The exact ratio of carbon dioxide to biomass that ends up in the final product depends on the type of plastic. For a polycarbonate this will be a molecular ratio of 1:1, but percentage of mass that comes directly from carbon dioxide depends on what the other monomer, the epoxide, is. However, the carbon in biomass comes from carbon dioxide in the atmosphere too, since that’s where the plants get their carbon by photosynthesis. So it depends how you want to look at it!

Perhaps the best example of plastics recycling is PET, which is the polyester used for drinks bottles that you probably already recycle at home. This is commonly recycled in two main ways: by breaking it down into its chemical components (monomers ethylene glycol and terephthalic acid) and then using them to make new polymer, or by melting the polymer and reshaping it into new products. Usually mechanical recycling, by melting the waste polymer and reshaping it, is used to turn PET packaging into fibres rather than drinks bottles to prevent the risk of any contamination getting into the food chain. Partially bio-based PET, like Coke’s Plant Bottles (see above) is chemically identical to ordinary PET and so can be recycled in the same way. More interestingly, there is a new fully-biobased alternative to PET, called PEF, where the oil-based terephthalic acid is replaced by a biobased furan-diacid. This can be melted and recycled in exactly the same way as PET and the normal recycling methods work perfectly well with a mixture of PET and biobased PEF. PEF is one of the most promising biobased plastics entering commercial production at the moment, and the way it can be easily recycled, even as a mixture with the PET, is one of the biggest reasons it is likely to be a success.

Questions for Nicky:

Would a bioeconomy actually be any more sustainable than what we have now? What about the pollution burning biofuels produces?

Although it’s impossible to predict all ends, sustainability is at the heart of all efforts to move towards a bioeconomy. Currently, we can think of the manufacturing economy as a line – crude oil and metals are extracted from the ground, they are processed into chemicals, fuels, and materials, and then we throw them away into landfill, or burn them. We know now that this model is highly unsustainable – if this goes on, we are going to use up all of our natural resources, pollute our land and oceans with our waste, and alter the Earth’s climate due to the release of CO2 from combustion. The good thing about a bio-based economy is that it works together with natural processes to ‘close the loop’ meaning that rather than a line, the process is circular. A biofuel will still release CO2 into the atmosphere when it is burnt. However, that CO2 will then be captured by plants that will then be processed into more biofuel… and so on, resulting in no NET difference in the levels of CO2 in the atmosphere (in theory).

In practice there are a number of things we have to consider – do the resources compete with food? Do they require a lot of land? Are the materials toxic – to humans, to fish, the environment as a whole? What about the transportation costs – financial and environmental? And the big question of waste – what happens at the end of the product life? Can it be reused, repurposed, recycled? Does it biodegrade, is it safe to burn? There are a lot of these types of questions to be answered and it is not always the case that bio-based products are ‘better’ than oil-based products by default. We have to check, and the system that has been developed to investigate these type of questions is called life cycle analysis (LCA). LCA considers a product from ‘cradle-to-grave’ or, better, from ‘cradle-to-cradle’, taking into account as many of these questions as possible, in order that we can get a true picture of the environmental impact of a product, and its potential replacements.

As a society we now take for granted the lifestyle that access to fuels, medicines, and materials that the chemical industries have produced. But this lifestyle was built on unsustainable practices. As a society, it will be unacceptable to do without these things in the future – and so the only way forward is to develop new, sustainable methods of production. This is what the bioeconomy, with the checks and balances that LCA provides, is all about.

Rather than chemical methods, are there any organisms that digest lignin into useful products?

Lignin in the environment is broken down mainly by fungi, although relevant enzymes have also recently been found in a bacterial species. Using enzymes to digest lignocellulose into ethanol is already real technology, however, this uses only the cellulose. There is real potential for using lignin-modifying enzymes found in nature, modified if necessary, to process lignin into useful products. However, it’s safe to say that this is at an early stage of investigation. Some creepy-crawlies can also digest wood, such as the termite, and the gribble – their mechanism for doing so is a matter of current research, including here at York in the Centre for Novel Agricultural products.

– contributed by Ian Ingram, Ruth Haley, Emily Johnston, and Nicky Egan


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